Photoprotective mixtures as imaging reagents in sequencing-by-synthesis

ABSTRACT

The invention relates to methods, compositions, devices, systems and kits as described including, without limitation, reagents and mixtures for determining the identity of nucleic acids in nucleotide sequences using, for example, sequencing by synthesis methods. In particular, the present invention contemplates the use of photoprotective mixture of compounds as imaging reagents to improve stability and storage of fluorescent compounds, including but not limited to, nucleotides with fluorescent labels.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a division of U.S. application Ser. No. 15/799,139,filed on Oct. 31, 2017, which claims priority to, and the benefit of,U.S. Provisional Application No. 62/419,702, filed on Nov. 9, 2016. Theentire contents of each of the above-identified applications is herebyincorporated by reference.

FIELD OF THE INVENTION

The invention relates to methods, compositions, devices, systems andkits as described including, without limitation, reagents and mixturesfor determining the identity of nucleic acids in nucleotide sequencesusing, for example, sequencing by synthesis methods. In particular, thepresent invention contemplates the use of photoprotective mixture ofcompounds as imaging reagents to improve stability and storage offluorescent compounds, including but not limited to, nucleotides withfluorescent labels.

BACKGROUND

Over the past 25 years, the amount of DNA sequence information that hasbeen generated and deposited into Genbank has grown exponentially.Traditional sequencing methods (e.g., for example Sanger sequencing) arebeing replaced by next-generation sequencing technologies that use aform of sequencing by synthesis (SBS), wherein specially designednucleotides and DNA polymerases are used to read the sequence ofchip-bound, single-stranded DNA templates in a controlled manner. Toattain high throughput, many millions of such template spots are arrayedacross a sequencing chip and their sequence is independently read outand recorded. Systems for using arrays for DNA sequencing are known(e.g., Ju et al., U.S. Pat. No. 6,664,079). However, there is acontinued need for methods and compositions for increasing theefficiency and/or reagent stability for sequencing nucleic acidsequences with automated sequencing.

SUMMARY OF THE INVENTION

The invention relates to methods, compositions, devices, systems andkits as described including, without limitation, reagents and mixturesfor determining the identity of nucleic acids in nucleotide sequencesusing, for example, sequencing by synthesis methods. In particular, thepresent invention contemplates the use of photoprotective reagentmixture of compounds as imaging reagents to improve stability andstorage of fluorescent compounds, including but not limited to,nucleotides with fluorescent labels.

In one embodiment, the present invention contemplates a photoprotectivemixture (e.g., a cocktail) of compounds as an imaging reagent during afluorophore detection step following nucleotide incorporation insequencing-by-synthesis (SBS). In one embodiment, the photoprotectivemixture comprises at least one effective antioxidant such as, but notlimited to, 2,5-dihydroxybenzoic acid (gentisic acid);3,4-dihydroxybenzoic acid (protocatechuic acid) or 3,4-dihydroxybenzoicacid ethyl ester (protocatechuate ethyl ester), at least onefluorescence quenching inhibitor such as, but not limited to,6-hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic acid (trolox) and atleast one radical scavenger such as, but not limited to, carnitine.

In one embodiment, the present invention contemplates, a method ofincorporating labeled nucleotides, comprising: a) providing; i) aplurality of nucleic acid primers and template molecules, ii) apolymerase, iii) an imaging reagent comprising a photoprotective mixtureof compounds, and iv) a plurality of nucleotide analogues wherein atleast a portion of said nucleotide analogues is labeled with a labelattached through a cleavable linker to the base; b) hybridizing (e.g.,under high stringency) at least a portion of said primers to at least aportion of said template molecules so as to create hybridized primers;c) incorporating a first labeled nucleotide analogue with saidpolymerase into at least a portion of said hybridized primers so as tocreate extended primers comprising an incorporated labeled nucleotideanalogue; and d) imaging said incorporated labeled nucleotide analoguein the presence of said imaging reagent. In one embodiment, the imagingreagent comprises a fluorescence quenching inhibitor. In one embodiment,the fluorescence quenching inhibitor is trolox. In one embodiment, thephotoprotective mixture comprises at least one antioxidant, at least onequenching inhibitor and at least one radical scavenger compound. In oneembodiment, the antioxidant is selected from the group consisting ofgentisic acid, protocatechuic acid and protocatechuate ethyl ester. Inone embodiment, the radical scavenger compound is carnitine. In oneembodiment, the method further comprises: e) incorporating a secondnucleotide analogue with said polymerase into at least a portion of saidextended primers. In one embodiment, the label is fluorescent.

In one embodiment, the present invention contemplates an imaging reagentcomprising at least one antioxidant, at least one fluorescence quenchinginhibitor and a buffer. In one embodiment, the antioxidant comprisescompounds selected from the group consisting of gentisic acid,protocatechuic acid and protocatechuate ethyl ester. In one embodiment,the imaging reagent further comprises a radical scavenger. In oneembodiment, the radical scavenger is carnitine. In one embodiment, thefluorescence quenching inhibitor is trolox. In one embodiment, thebuffer is a TRIS buffer. In one embodiment, the buffer is a HEPESbuffer.

In one embodiment, the present invention contemplates a kit, comprisingi) a first container comprising an imaging reagent comprising at leastone antioxidant, at least one fluoresence quenching inhibitor and abuffer; and ii) a second container comprising a plurality of nucleotideanalogues wherein at least a portion of said nucleotide analogues islabeled with a label attached through a cleavable linker to the base. Inone embodiment, the imaging reagent further comprises a radicalscavenger. In one embodiment, the radical scavenger is carnitine. In oneembodiment, the fluorescence quenching inhibitor is trolox. In oneembodiment, the buffer is a TRIS buffer. In one embodiment, the bufferis a HEPES buffer.

In one embodiment, the present invention contemplates a systemcomprising a solution of primers hybridized to a template comprising aplurality of nucleotide analogues attached to a cleavable label and animaging reagent comprising at least one antioxidant, at least onefluorescent quenching inhibitor and a buffer. In one embodiment, thehybridized primers and said template are immobilized. In one embodiment,the hybridized primers and said template are in a flow cell. In oneembodiment, the imaging reagent further comprises a radical scavenger.In one embodiment, the radical scavenger is carnitine. In oneembodiment, the fluorescence quenching inhibitor is trolox. In oneembodiment, the buffer is a TRIS buffer. In one embodiment, the bufferis a HEPES buffer.

In one embodiment, the present invention contemplates an imaging reagentcomprising: i) a TRIS HCl buffer; ii) carnitine ranging in concentrationbetween approximately 5-50 mM; iii) trolox ranging in concentrationbetween approximately 5-15 mM; iv) 2,5 dihydroxybenzoic acid ranging inconcentration between approximately 10-50 mM; and v) 3,4,dihydroxybenzoic acid ethyl ester ranging in concentration betweenapproximately 10-20 mM.

Definitions

To facilitate the understanding of this invention, a number of terms aredefined below. Terms defined herein have meanings as commonly understoodby a person of ordinary skill in the areas relevant to the presentinvention. Terms such as “a”, “an” and “the” are not intended to referto only a singular entity but also plural entities and also includes thegeneral class of which a specific example may be used for illustration.The terminology herein is used to describe specific embodiments of theinvention, but their usage does not delimit the invention, except asoutlined in the claims.

The term “about” as used herein, in the context of any of any assaymeasurements refers to +/−5% of a given measurement.

The term “imaging reagent” as used herein, refers to a mixture ofcompounds that are capable of enhancing label emission intensity and/orimproving fluorophore detection by at least an order of magnitude. Whilenot intending to limit the invention to any particular mechanism, it isbelieved that the herein described mixtures enhance signal-to-noiseratios, or reduce photobleaching and/or fluorophore “blinking.” Oneclass of compounds that are useful in imaging reagents are fluorescencequenching inhibitors.

The term “fluorescence quenching inhibitor” as used herein, refer to aclass of compounds that improve the signal quality of fluorescentlabels. Without being bound to any mechanim, it is believed that suchcompounds work by reacting with oxidation compounds that result in aquenching of the fluorescent signal by non-specific photo-bleachingphenomenon. For example, one such compound is trolox(6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid).

The term “mixture” or “cocktail” as used herein interchangeably, refersto a plurality of compounds (generally in a solution, such as a buffersolution) that together create an imaging reagent for the purpose ofdetecting labeled nucleotide analogues within a nucleotide sequence.

The term “photoprotective” as used herein, refers to an end result of animaging reagent mixture or cocktail that enhances stability and storageshelf-life of fluorescent compounds. Without being bound by theory, itis believed that they work by protecting against: i) photo-bleaching ofnucleotide fluorescent labels; ii) signal quenching; and iii)radically-induced DNA photo-damage and photo-scission.

The term “antioxidant compounds” as used herein, refers to a moleculethat inhibits a chemical reaction that can produce free radicals, Forexample, many vitamins (e.g., vitamin E and vitamin C), in addition tocertain enzymes (catalase and superoxide dismutase) are naturallyoccuring antioxidants. Other chemicals also have these propertiesincluding, but not limited to, gentisic acid, protocatechuic acid and/orprotocatechuate ethyl ester.

The term “radical scavenger compound” as used herein, refers to amolecule that remove or de-activate impurities and unwanted reactionproducts, for example oxygen. While radical scavenger compounds have anantioxidant end result, it is believed that they function by a differentmechanism than antioxidant compounds. For example, one such radicalscavenger compound includes, but is not limited to, tocopherol,carnitine and/or naringenin. Even so, it is known that some radicalscavenger compounds have other biochemical activities, for example,antioxidant activities and singlet oxygen quenching.

The term “buffer” as used herein, refers to a mixture of basic salts anda hydrogen exchange compound (either a weak acid or a weak base) thatcan maintain a stable pH level over a wide range of environmentalconditions (e.g., temperature, salinity), including changes in hydrogenion concentration. For example, such buffers may include, but are notlimited to 4-(2-hydroxyethyl) -1-piperazineethanesulfonic acid (HEPES)buffer and/or tris(hydroxymethyl)-aminomethane (TRIS) buffer.

The term “linker” as used herein, refers to any molecule (or collectionof molecules) capable of attaching a label and/or chemical moiety thatis susceptible to cleavage. In one embodiment, cleavage of the linkermay produce toxic radical products. For example, a linker may include,but is not limited to, a disulfide linker and/or an azide linker.

The term “attached” as used herein, refers to any interaction between afirst molecule (e.g., for example, a nucleic acid) and a second molecule(e.g., for example, a label molecule). Attachment may be reversible orirreversible. Such attachment includes, but is not limited to, covalentbonding, ionic bonding, Van der Waals forces or friction, and the like.

“Nucleic acid sequence” and “nucleotide sequence” as used herein referto an oligonucleotide or polynucleotide, and fragments or portionsthereof, and to DNA or RNA of genomic or synthetic origin which may besingle- or double-stranded, and represent the sense or antisense strand.Such nucleic acids may include, but are not limited to, cDNA, mRNA orother nucleic acid sequences.

The term “an isolated nucleic acid”, as used herein, refers to anynucleic acid molecule that has been removed from its natural state(e.g., removed from a cell and is, in a preferred embodiment, free ofother genomic nucleic acid).

In some embodiments, the present invention contemplates hybridizingnucleic acid together. This requires some degree of complementarity. Asused herein, the terms “complementary” or “complementarity” are used inreference to “polynucleotides” and “oligonucleotides” (which areinterchangeable terms that refer to a sequence of nucleotides) relatedby the base-pairing rules. For example, the sequence “C-A-G-T,” iscomplementary to the sequence “G-T-C-A.” Complementarity can be“partial” or “total.” “Partial” complementarity is where one or morenucleic acid bases is not matched according to the base pairing rules.“Total” or “complete” complementarity between nucleic acids is whereeach and every nucleic acid base is matched with another base under thebase pairing rules. The degree of complementarity between nucleic acidstrands has significant effects on the efficiency and strength ofhybridization between nucleic acid strands. This is of particularimportance in amplification reactions, as well as detection methodswhich depend upon binding between nucleic acids.

The terms “homology” and “homologous” as used herein in reference tonucleotide sequences refer to a degree of complementarity with othernucleotide sequences. There may be partial homology or complete homology(i.e., identity). A nucleotide sequence which is partiallycomplementary, i.e., “substantially homologous,” to a nucleic acidsequence is one that at least partially inhibits a completelycomplementary sequence from hybridizing to a target nucleic acidsequence. The inhibition of hybridization of the completelycomplementary sequence to the target sequence may be examined using ahybridization assay (Southern or Northern blot, solution hybridizationand the like) under conditions of low stringency. A substantiallyhomologous sequence or probe will compete for and inhibit the binding(i.e., the hybridization) of a completely homologous sequence to atarget sequence under conditions of low stringency. This is not to saythat conditions of low stringency are such that non-specific binding ispermitted; low stringency conditions require that the binding of twosequences to one another be a specific (i.e., selective) interaction.The absence of non-specific binding may be tested by the use of a secondtarget sequence which lacks even a partial degree of complementarity(e.g., less than about 30% identity); in the absence of non-specificbinding the probe will not hybridize to the second non-complementarytarget.

Low stringency conditions comprise conditions equivalent to binding orhybridization at 42° C. in a solution consisting of 5 x SSPE (43.8 g/lNaCl, 6.9 g/l NaH2PO4·H2O and 1.85 g/l EDTA, pH adjusted to 7.4 withNaOH), 0.1% SDS, 5x Denhardt's reagent {50x Denhardt's contains per 500ml: 5 g Ficoll (Type 400, Pharmacia), 5 g BSA (Fraction V; Sigma)} and100 μg/ml denatured salmon sperm DNA followed by washing in a solutioncomprising 5x SSPE, 0.1% SDS at 42° C. when a probe of about 500nucleotides in length is employed. Numerous equivalent conditions mayalso be employed to comprise low stringency conditions; factors such asthe length and nature (DNA, RNA, base composition) of the probe andnature of the target ( DNA, RNA, base composition, present in solutionor immobilized, etc.) and the concentration of the salts and othercomponents (e.g., the presence or absence of formamide, dextran sulfate,polyethylene glycol), as well as components of the hybridizationsolution may be varied to generate conditions of low stringencyhybridization different from, but equivalent to, the above listedconditions. In addition, conditions which promote hybridization underconditions of high stringency (e.g., increasing the temperature of thehybridization and/or wash steps, the use of formamide in thehybridization solution, etc.) may also be used.

As used herein, the term “hybridization” is used in reference to thepairing of complementary nucleic acids using any process by which astrand of nucleic acid joins with a complementary strand through basepairing to form a hybridization complex. Hybridization and the strengthof hybridization (i.e., the strength of the association between thenucleic acids) is impacted by such factors as the degree ofcomplementarity between the nucleic acids, stringency of the conditionsinvolved, the Tm of the formed hybrid, and the G:C ratio within thenucleic acids.

As used herein the term “hybridization complex” refers to a complexformed between two nucleic acid sequences by virtue of the formation ofhydrogen bounds between complementary G and C bases and betweencomplementary A and T bases; these hydrogen bonds may be furtherstabilized by base stacking interactions. The two complementary nucleicacid sequences hydrogen bond in an antiparallel configuration. Ahybridization complex may be formed in solution (e.g., CO t or RO tanalysis) or between one nucleic acid sequence present in solution andanother nucleic acid sequence immobilized to a solid support (e.g., anylon membrane or a nitrocellulose filter as employed in Southern andNorthern blotting, dot blotting or a glass slide as employed in in situhybridization, including FISH (fluorescent in situ hybridization)).

As used herein, the term “Tm ” is used in reference to the “meltingtemperature.” The melting temperature is the temperature at which apopulation of double-stranded nucleic acid molecules becomes halfdissociated into single strands. As indicated by standard references, asimple estimate of the Tm value may be calculated by the equation:Tm=81.5+0.41 (% G+C), when a nucleic acid is in aqueous solution at 1MNaCl. Anderson et al., “Quantitative Filter Hybridization” In: NucleicAcid Hybridization (1985). More sophisticated computations takestructural, as well as sequence characteristics, into account for thecalculation of Tm.

As used herein the term “stringency” is used in reference to theconditions of temperature, ionic strength, and the presence of othercompounds such as organic solvents, under which nucleic acidhybridizations are conducted. “Stringency” typically occurs in a rangefrom about

Tm to about 20° C. to 25° C. below Tm. A “stringent hybridization” canbe used to identify or detect identical polynucleotide sequences or toidentify or detect similar or related polynucleotide sequences. Forexample, when fragments are employed in hybridization reactions understringent conditions the hybridization of fragments which contain uniquesequences (i.e., regions which are either non-homologous to or whichcontain less than about 50% homology or complementarity) are favored.Alternatively, when conditions of “weak” or “low” stringency are usedhybridization may occur with nucleic acids that are derived fromorganisms that are genetically diverse (i.e., for example, the frequencyof complementary sequences is usually low between such organisms).

As used herein, the term “amplifiable nucleic acid” is used in referenceto nucleic acids which may be amplified by any amplification method. Itis contemplated that “amplifiable nucleic acid” will usually comprise“sample template.”

As used herein, the term “sample template” or (more simply) “template”refers to nucleic acid originating from a sample which is analyzed forthe presence of a target sequence of interest. In contrast, “backgroundtemplate” is used in reference to nucleic acid other than sampletemplate which may or may not be present in a sample. Backgroundtemplate is most often inadvertent. It may be the result of carryover,or it may be due to the presence of nucleic acid contaminants sought tobe purified away from the sample. For example, nucleic acids fromorganisms other than those to be detected may be present as backgroundin a test sample.

“Amplification” is defined as the production of additional copies of anucleic acid sequence and is generally carried out using polymerasechain reaction. Dieffenbach C. W. and G. S. Dveksler (1995) In: PCRPrimer, a Laboratory Manual, Cold Spring Harbor Press, Plainview, N.Y.

As used herein, the term “polymerase chain reaction” (“PCR”) refers tothe method of K. B. Mullis U.S. Pat. Nos. 4,683,195 and 4,683,202,herein incorporated by reference, which describe a method for increasingthe concentration of a segment of a target sequence in a mixture ofgenomic DNA without cloning or purification. The length of the amplifiedsegment of the desired target sequence is determined by the relativepositions of two oligonucleotide primers with respect to each other, andtherefore, this length is a controllable parameter. By virtue of therepeating aspect of the process, the method is referred to as the“polymerase chain reaction” (hereinafter “PCR”). Because the desiredamplified segments of the target sequence become the predominantsequences (in terms of concentration) in the mixture, they are said tobe “PCR amplified”. With PCR, it is possible to amplify a single copy ofa specific target sequence in genomic DNA to a level detectable byseveral different methodologies (e.g., hybridization with a labeledprobe; incorporation of biotinylated primers followed by avidin-enzymeconjugate detection; incorporation of 32P-labeled deoxynucleotidetriphosphates, such as dCTP or dATP, into the amplified segment). Inaddition to genomic DNA, any oligonucleotide sequence can be amplifiedwith the appropriate set of primer molecules. In particular, theamplified segments created by the PCR process itself are, themselves,efficient templates for subsequent PCR amplifications.

As used herein, the term “primer” refers to an oligonucleotide, whetheroccurring naturally as in a purified restriction digest or producedsynthetically, which is capable of acting as a point of initiation ofsynthesis when placed under conditions in which synthesis of a primerextension product which is complementary to a nucleic acid strand isinduced, (i.e., in the presence of nucleotides and an inducing agentsuch as DNA polymerase and at a suitable temperature and pH). The primeris preferably single stranded for maximum efficiency in amplification,but may alternatively be double stranded. If double stranded, the primeris first treated to separate its strands before being used to prepareextension products. Preferably, the primer is anoligodeoxy-ribonucleotide. The primer must be sufficiently long to primethe synthesis of extension products in the presence of the inducingagent. The exact lengths of the primers will depend on many factors,including temperature, source of primer and the use of the method.

As used herein, the term “probe” refers; to an oligonucleotide (i.e., asequence of nucleotides), whether occurring naturally as in a purifiedrestriction digest or produced synthetically, recombinantly or by PCRamplification, which is capable of hybridizing to anotheroligonucleotide of interest. A probe may be single-stranded ordouble-stranded. Probes are useful in the detection, identification andisolation of particular gene sequences. It is contemplated that anyprobe used in the present invention will be labeled with any “reportermolecule,” so that is detectable in any detection system, including, butnot limited to enzyme (e.g., ELISA, as well as enzyme-basedhistochemical assays), fluorescent, radioactive, and luminescentsystems. It is not intended that the present invention be limited to anyparticular detection system or label.

The term “label” or “detectable label” are used herein, to refer to anycomposition detectable by spectroscopic, photochemical, biochemical,immunochemical, electrical, optical or chemical means. Such labelsinclude biotin for staining with labeled streptavidin conjugate,magnetic beads (e.g., Dynabeads®), fluorescent dyes (e.g., fluorescein,texas red, rhodamine, green fluorescent protein, and the like),radiolabels (e.g., 3H, 125I, 35S, 14C, or 32P), enzymes (e.g., horseradish peroxidase, alkaline phosphatase and others commonly used in anELISA), and calorimetric labels such as colloidal gold or colored glassor plastic (e.g., polystyrene, polypropylene, latex, etc.) beads.Patents teaching the use of such labels include, but are not limited to,U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437;4,275,149; and 4,366,241 (all herein incorporated by reference).

In a preferred embodiment, the label is typically fluorescent and islinked to the base of the nucleotide. For cytosine and thymine, theattachment is usually to the 5-position. For the other bases, a deazaderivative is created and the label is linked to a 7-position ofdeaza-adenine or deaza-guanine.

The labels contemplated in the present invention may be detected by manymethods. For example, radiolabels may be detected using photographicfilm or scintillation counters, fluorescent markers may be detectedusing a photodetector to detect emitted light. Enzymatic labels aretypically detected by providing the enzyme with a substrate anddetecting, the reaction product produced by the action of the enzyme onthe substrate, and calorimetric labels are detected by simplyvisualizing the colored label.

The term “luminescence” and/or “fluorescence”, as used herein, refers toany process of emitting electromagnetic radiation (light) from anobject, chemical and/or compound. Luminescence and/or fluorescenceresults from a system which is “relaxing” from an excited state to alower state with a corresponding release of energy in the form of aphoton. These states can be electronic, vibronic, rotational, or anycombination of the three. The transition responsible for luminescencecan be stimulated through the release of energy stored in the systemchemically or added to the system from an external source. The externalsource of energy can be of a variety of types including, but not limitedto, chemical, thermal, electrical, magnetic, electromagnetic, physicalor any other type capable of causing a system to be excited into a statehigher than the ground state. For example, a system can be excited byabsorbing a photon of light, by being placed in an electrical field, orthrough a chemical oxidation-reduction reaction. The energy of thephotons emitted during luminescence can be in a range from low-energymicrowave radiation to high-energy x-ray radiation. Typically,luminescence refers to photons in the range from UV to IR radiation.

BRIEF DESCRIPTION OF THE FIGURES

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

FIG. 1A-B presents a comparative workflow between a conventional imagingbuffer configuration and photoprotective imaging buffer configuration.

FIG. 1A: An illustrative workflow for a conventional imaging buffer kitconfiguration.

FIG. 1B: A photoprotective imaging buffer kit configuration comprisingnew and improved Cleave and Imaging Buffer Consumables.

FIG. 2 presents exemplary data showing that SBS metrics are comparablebetween a conventional imaging buffer and a Photoprotective imagingbuffer 7B.

FIG. 3A-D presents exemplary data showing comparative read lengthdistributions between a conventional imaging buffer and aPhotoprotective imaging buffer 7B subsequent to each SBS run.

FIG. 3A: Run 8.3

FIG. 3B; Run 8.5

FIG. 3C; Run 8.6

FIG. 3D: Run 8.41 (retest)

FIG. 4A-D presents exemplary data showing raw error plots between aconventional imaging buffer and a Photoprotective imaging buffer 7Bsubsequent to each SBS run.

FIG. 4A: Run 8.3

FIG. 4B; Run 8.5

FIG. 4C; Run 8.6

FIG. 4D: Run 8.41 (retest)

FIG. 5 presents exemplary data showing a comparison of average readlength data between a conventional imaging buffer (IB_Baseline) andthree (3) versions of a Photoprotective imaging buffer SC-P version 9.

FIG. 6A-C presents exemplary data showing a comparison of raw error plotdata between a conventional imaging buffer (IB_Baseline) and three (3)versions of a Photoprotective imaging buffer SC-P version 9.

FIG. 6A: Photoprotective imaging buffer SC-P 9.

FIG. 6B: Photoprotective imaging buffer SC-P 9B.

FIG. 6C: Photoprotective imaging buffer SC-P 9C.

FIG. 7 presents exemplary data showing the effect of lower ionic andaromatic compound concentrations in an imaging buffer on nucleotidesignal retention.

FIG. 8 presents exemplary data showing raw error rates in sequencingruns using SC-P9C imaging reagent versus a baseline IB.

FIG. 9A-B presents exemplary data showing raw error rates in sequencingruns using SC-P9C imaging reagent formulated with either a HEPES bufferor a TRIS buffer versus a baseline IB.

FIG. 9A: Results using a HEPES buffer.

FIG. 9B: Results using a TRIS buffer.

FIG. 10 presents exemplary data showing the effects of carnitineconcentration on MFST data output in both 101x gene panels (blue) andBRCA gene panels (red).

FIG. 11 presents exemplary data showing the effects of carnitineconcentration on percent perfect parameters in both 101x gene panels(blue) and BRCA gene panels (red).

FIG. 12 presents exemplary data showing the effects of carnitineconcentration on average read length in both 101x gene panels (blue) andBRCA gene panels (red).

FIG. 13 presents exemplary data showing the effects of carnitineconcentration on percent error rate in both 101x gene panels (blue) andBRCA gene panels (red).

FIG. 14A-B presents exemplary data showing the effects of carnitineconcentration on raw error rate in both 101x gene panels (blue) and BRCAgene panels (red).

FIG. 14A: SC-9 IB and SC9B IB versus reference IB.

FIG. 14B: SC-9D D3 versus reference IB.

FIG. 15A-B presents exemplary data showing the effects of carnitineconcentration on read length distribution in both 101x gene panels(blue) and BRCA gene panels (red).

FIG. 15A: SC-9 IB and SC9B IB versus reference IB.

FIG. 15B: SC-9D D3 versus reference IB.

FIG. 16 presents exemplary data showing the effects of carnitineconcentration on nucleotide signal retention in both 101x gene panels(blue) and BRCA gene panels (red).

DETAILED DESCRIPTION OF THE INVENTION

The invention relates to methods, compositions, devices, systems andkits as described including, without limitation, reagents and mixturesfor determining the identity of nucleic acids in nucleotide sequencesusing, for example, sequencing by synthesis methods. In particular, thepresent invention contemplates the use of photoprotective buffer mixtureof compounds as imaging reagents to improve stability and storage offluorescent compounds, including but not limited to, nucleotides withfluorescent labels.

In one embodiment, the present invention contemplates compositionscomprising photoprotective mixtures as imaging reagents duringsequencing-by-synthesis (SBS). In one embodiment, a method comprisingimaging occurs during a fluorophore detection step. In one embodiment, amethod comprising imaging occurs following nucleotide incorporation. Inone embodiment, a photoprotective mixtures comprises compounds such as,but not limited to: carnitine;6-hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic Acid (trolox);2,5-dihydroxybenzoic acid (gentisic acid); 3,4-dihydroxybenzoic acid(protocatechuic acid); 3,4-dihydroxybenzoic acid ethyl ester(protocatechuate ethyl ester), 4-hydroxycinnamic acid,3,4-dihydroxybenzeneacrylic acid, 1,4-diazabicyclo[2.2.2]octane (DABCO),lipoic acid and/or acetyl-carnitine.

In one embodiment, the present invention contemplates a method forsequencing a 150 bp read length. Other significant additional benefitsare also provided including, but not limited to: improved manufacturing,storage and quality control processes, improved usability through userfriendly kit concept and workflow, improved instrument reliability dueto delivery of a single component solution that does not require mixingof individual components through next generation sequencing platformfluidics.

I. Sequencing-By-Synthesis (SBS)

In one embodiment, the present invention contemplates a series of methodsteps performed by an automated sequencing by synthesis instrument(e.g., a next generation sequencing platform). See U.S. Pat. No.9,145,589, hereby incorporated by reference. In one embodiment, theinstrument is comprised of numerous reagent reservoirs. Each reagentreservoir has a specific reactivity reagent dispensed within thereservoir to support the SBS process, for example:

In one embodiment, the SBS method comprises doing different steps atdifferent stations. By way of example, each station is associated with aparticular step. While not limited to particular formulations, someexamples for these steps and the associated reagents are shown below:

1) Extend A Reagent: Comprises reversibly terminated labeled nucleotidesand polymerase. One composition of Extend A may be as follows:

Component Concentration PNSE (% wt/vol) 0.005% Tris × HC1 (pH 8.8), mM50 NaCl (mM) 50 EDTA (mM) 1 MgSO4 (mM) 10 Cystamine (mM) 1 Glycerol (%wt/vol) 0.01% Therminator IX* (U/ml) 10 N3-dCTP (μM) 3.83 N3-dTTP (μM)3.61 N3-dATP (μM) 4.03 N3-dGTP (μM) 0.4 Alexa488-dCTP (nM) 550 R6G-dUTP(nM) 35 ROX-dATP (nM) 221 Cy5-dGTP (nM) 66 *with Alkylated free Cysteine2) Extend B Reagent: Comprises reversibly terminated unlabelednucleotides and polymerase, but lacks labeled nucleotide analogues. Onecomposition of Extend B may be as follows:

Component Concentration PNSE (% wt/vol) 0.005% Tris × HCl (pH 8.8), mM50 NaCl (mM) 50 EDTA (mM) 1 MgSO4 (mM) 10 Glycerol (% wt/vol) 0.01%Therminator IX* (U/ml) 10 N3-dCTP (μM) 21 N3-dTTP (μM) 17 N3-dATP (μM)21 N3-dGTP (μM) 2 *Alkylated free Cysteine3) Wash solution 1 with a detergent (e.g., polysorbate 20) citratebuffer (e.g., saline)

s4) Cleave Reagent: One cleaving solution composition may be as follows:

Component Concentration NaOH (mM) 237.5 TrisHCl (pH 8.0) (mM) 237.5 TCEP(mM) 505) Wash solution 2 with a detergent (e.g., polysorbate 20) atris(hydroxymethyl)-aminomethane (Tris) buffer.

II. Conventional Imaging Solutions

One enzymatic formulation currently being used as an imaging reagent(IB) comprises four-components. These four components comprise HEPESbuffer, glucose oxidase, glucose and trolox and are required to becombined to create two separate solutions prior to supporting an

SBS method. These two solutions are kept separate throughout thesequencing process to prevent glucose oxidase and glucose from reactingprematurely with oxygen causing degradation of the enzymatic system andelimination of H₂O₂. These two final solutions are mixed during SBSthrough a mixing valve at every imaging step before introduction into aflow cell. Use of this type of imaging method step, albeit effective,presents challenges in several areas including, but not limited to: i)stability of the manufacturing process; ii) maintaining quality controldue to complicated exo/endo specification paradigms; iii) difficultusability due to a complex kit configuration and workflow; iv) limitedinstrument reliability due to delivery volume failure modes due tomixing valve reliability issues. As seen herein, the conventional orbaseline imaging reagent (IB) has been used for performance benchmarkingof various embodiments of the presently disclosed photoprotectivemixture imaging reagents .

III. Photoprotective Imaging Solutions

In one embodiment, effective imaging solutions and buffer formulationsfor SBS methods comprise molecular components that ensurephotoprotection during light exposure. While not bound by theory, it isbelieved that they prevent three main phenomena: i) photo-bleaching ofnucleotide fluorescent labels; ii) signal quenching; and iii)radically-induced DNA photo-damage and photo-scission. Imaging solutionscan be formulated either as either enzymatic systems or mixturescomprising a variety of chemical mixtures such as mixtures including,but not limited to, a molecular oxygen “sink”, an antioxidant/radicalscavenger and a singlet oxygen quencher. Some of the components in thesemixtures also provide additional protection against oxidative stress anddegradation of the imaging solution upon prolonged storage.

Although it is not necessary to understand the mechanism of an inventionit is believed that a “mixture” or “cocktail” approach is most suitablefor formulating long shelf-life imaging solutions because it bestsupports a variety of functional aspects pertaining to product designrobustness, ranging from functional performance and formulationstability to manufacturability, usability and storage.

In one embodiment, the present invention contemplates a photoprotectivemixture as an imaging reagent during a fluorophore detection stepfollowing nucleotide incorporation in sequencing-by-synthesis (SBS).These photoprotective mixture imaging reagents comprise an effectiveantioxidant such as, but not limited to, 2,5-dihydroxybenzoic acid(gentisic acid); 3,4-dihydroxybenzoic acid (protocatechuic acid) or3,4-dihydroxybenzoic acid ethyl ester (protocatechuate ethyl ester), afluorescence quenching inhibitor such as, but not limited to, 6-hydroxy-2,5,7, 8-tetramethylchromane-2-carboxylic acid (trolox) and a radicalscavenger (e.g., carnitine), an antioxidant and/or a singlet oxygenquencher.

In one embodiment, the photoprotective cocktail comprises a mixture(e.g., imaging reagent SC-P 7B) including the components:

In one embodiment, the photoprotective cocktail comprises a mixture(e.g., imaging reagent SC-P 9C) including the components:

Photoprotective cocktail mixtures, exemplified by those above, have beendesigned with properties including, but not limited to, photoprotection,stability, manufacturability, long shelf-life storage and usability.These mixtures are also designed for compatibility with off the shelfsequencing kits (i.e., the GeneReader® 1.1 sequencing kit). Inparticular, carnitine has been found to induce reduction of oxidativestress and preservation of chemical activity and/or biological functionafter long term storage of biological fluids and functional buffers.Without being bound by theory, carnitine can conceivably supportenhanced storage of complex molecular mixtures due to reduction ofoxidative stress caused by molecules including, but not limited to,oxygen, peroxy radicals, or singlet oxygen. Although it is not necessaryto understand the mechanism of an invention, it is believed thatcompounds such as carnitine preserve their protective properties, evenupon prolonged storage as a formulation, including but not limited tomolecular reduced states and stability against chemical bond scission(e.g., radical- or photo-scission).

The data presented herein demonstrates an interrogation potential forvarious photoprotective imaging mixtures of compounds as imagingreagents. Additionally, full compatibility with SBS instrument hardwareis verified for all components as observed from an inspection of bothinstrument and liquid waste at the end of sequencing. Improvements ofthe presently disclosed photoprotective mixture imaging reagents areexemplified with comparative sequencing workflows.

For example, a prospective kit configuration for photoprotective mixtureimaging reagents is shown as a single component consumable stored in akit box compatible with −20° C. storage conditions. See, FIG. 1. Ancomparative workflow for a conventional imaging reagent kitconfiguration (FIG. 1A) demonstrates the increased complexity as opposedto the presently disclosed photoprotective imaging reagent kitconfiguration (FIG. 1B). Although it is not necessary to understand themechanism of an invention, it is believed that the presently disclosedphotoprotective imaging reagent kit configuration greatly improvesusability during an SBS method by decreasing the number of componentsrequired in the kit and workflow.

Photoprotective imaging reagents as contemplated by the presentinvention have been tested for long read length sequencing performance(e.g., approximately 150 bp). Some of these tests entailed 157 cyclesequencing and a head-to-head comparison of photoprotective mixtureimaging reagents to a conventional imaging reagent (e.g., baseline D3reagent). Studies were performed using Gene Reader instruments and twotypes of DNA libraries, i.e., NA12878/101X gene panel and NA12878/BRCAgene panel. Sequencing metrics were analyzed to provide comparativesystem performance indicators, e.g., raw error rate, average readlength, output (Gb).

For example, GDP4 Testing was performed using the photoprotectiveimaging buffer reagent SC-P 7B made in accordance with Example II. Thetesting was run using an APF protocol v2 comprising 157 cycles and 130tiles utilizing the SP101x gene panel. Of the four runs (e.g., 8.41)that was performed was deemed to be invalid and retested (noted as “**).It can be seen that the conventional imaging reagent (Baseline IB) and aphotoprotective imaging reagent SC-P 7B were comparable across allsequencing metrics. See, FIG. 2 and Table 1.

TABLE 1 Comparative Sequencing Metrics: Conventional IB (Baseline)versus C-P 7B IB. Sample Output Date Run GR ID (MFST) Beads/tiles Errorrate % Live Mar. 25, 2016 IB 7B 8.5 SP101x 1.77127963 429218.1690.747583 48% Apr. 15, 2016 IB 7B 8.41 SP101x 1.904151381 428153.6250.775358 50% Retest** Apr. 5, 2016 IB 7B 8.6 SP101x 1.87757536440901.246 0.751118 49% Apr. 11, 2016 IB 7B 8.3 SP101x 2.052871269444646.646 0.728655 51% 1.901 435729 0.75% 49% Mar. 28, 2016 Baseline8.5 SP101x 1.852687368 434523.031 0.795124 48% Mar. 28, 2016 Baseline8.41 SP101x 1.808064963 435729 0.77365 49% Apr. 8, 2016 Baseline 8.6SP101x 1.890117702 438295.854 0.803485 51% Apr. 14, 2016 Baseline 8.3SP101x 2.023612666 431433.115 0.778109 52% 1.893 434999 0.79% 49% % %Date Mapped Polyclonal % Perfect AVG RL Lead Lag Mar. 25, 2016 29% 36%0.5955009 109.6339 0.337969 0.1115 Apr. 15, 2016 31% 35% 0.5969785110.6978 0.405625 0.084068 Apr. 5, 2016 30% 34% 0.5990981 108.72610.347992 0.098931 Apr. 11, 2016 31% 35% 0.6067697 113.2278 0.4065380.117338 30% 35% 59% 110 0.374 0.102 Mar. 28, 2016 29% 36% 0.5857853112.4275 0.4325 0.123562 Mar. 28, 2016 29% 37% 0.5958026 110.35990.424246 0.126323 Apr. 8, 2016 31% 36% 0.583074 108.433 0.3479920.098931 Apr. 14, 2016 31% 36% 0.5949944 115.0466 0.409185 0.157954 30%36% 58% 111 0.399 0.149

These data show that the metric, lag, shows the only statisticallyrelevant difference between the two imaging reagents with a 30% lowerlag when tested with a photoprotective imaging reagent SC-P 7B. The readlength distributions among the four runs were equivalent when testedbetween the two imaging reagents. See, FIGS. 3A-3D. The raw error plotsamong the four runs were also equivalent when tested between the twoimaging reagents. See, FIGS. 4A-4D.

Testing was also performed using various embodiments of the exemplaryphotoprotective imaging reagent 9CV2T made in accordance with ExampleIII. Three different versions of the 9CV2T reagents were made. Althoughit is not necessary to understand the mechanism of an invention, it isbelieved that at least one of these reagents resulted in an improvedsignal retention. For example, three of the tested versions of 9CV2Timaging reagents comprised:

SC-P9 pH 8.5

Tris 50 mM L-Carnitine 50 mM Trolox 15 mM Protocatechuic acid 20 mMethyl esteror,

SC-P9B pH 8.5

Tris 50 mM L-Carnitine 15 mM Trolox 15 mM Protocatechuic acid 20 mMethyl esterand,

SC-P9C pH 8.5

Tris 50 mM L-Carnitine 15 mM Trolox 15 mM Protocatechuic acid ethyl 10mM ester

A comparison of basic sequencing metrics was made between these threeSC-P version 9CV2T imaging reagents and the conventional IB reagent witha sequencing protocol of 137 cycles using a Vaccinia virus (VACV) strainTianTan TP03 genome. See, Table 2.

TABLE 2 Comparison of Sequencing Metrics Between SC-P Version 9 IBs AndA Conventional IB (IB_Baseline). Output Error Rate Run Name GR/Sample(MFST) % Mapped AVG RL (MFST) % Perfect Lead Lag IB _Baseline 8.26/TP031.23E+09 32.6% 99.5 0.60% 67.6% 0.421 0.125 IB_SC-P9 8.26/TP03 1.21E+0933.1% 98.5 0.54% 69.00%  0.407 0.116 IB_SC-P9B 8.26/TP03 1.16E+09 31.8%98.9 0.54% 69.1% 0.389 0.124 IB_SC-P9C 8.17/TP03 1.12E+09 30.6% 99.70.58% 67.5% 0.432 0.093A relative equivalency was seen between these SC-P version 9CV2T imagingreagents and the baseline imaging reagent with respect to average readlength. See, FIG. 5. Such equivalency was also observed for the raw dataplots between the SC-P version 9CV2T imaging reagents and the baselineimaging reagent. See, FIGS. 6A-C. These data demonstrate that loweringof concentrations of ionic and aromatic compound (e.g., carnitine andprotocatechuic acid, respectively), does improve signal retention. See,FIG. 7. Although it is not necessary to understand the mechanism of aninvention, it is believed that this observation is likely due tomitigated signal quenching which usually arises from interactionsbetween fluorophores and aromatic/ionic species in a photoprotectivebuffer.

The SC-P9C imaging reagent was used in a 157 cycles non-APF/88 tileprotocol on a BRCA gene panel (runs 8.17; 8.24; 8.26). The sequencingmetrics were compared to a reference imaging IB. See, Table 3.

TABLE 3 Sequence Metrics Comparison Of SC-P9C To Baseline IB On A BRCAGene Panel Output % % % AVG Error % Run Condition GR Run date Type(MFST) Beads/tile Live Mapped Polyclonal RL (MFST) Perfect Lead LagBaseline_BRCA 8.17 Apr. 15, 2016 HG19 1.14E+09 426294 47% 26% 41% 115.00.72% 58% 0.513 0.060 BRCA Baseline_BRCA 8.17 Apr. 15, 2016 HG191.17E+09 424933 45% 27% 38% 114.0 0.74% 57% 0.466 0.091 BRCA Prototype9C_BRCA 8.26 Apr. 15, 2016 HG19 1.09E+09 428096 44% 26% 36% 110.0 0.78%53% 0.477 0.061 BRCA Prototype 9C_BRCA 8.26 Apr. 15, 2016 HG19 1.14E+09422093 45% 26% 36% 112.0 0.79% 54% 0.446 0.084 BRCA Prototype 9C_BRCA8.24 Apr. 15, 2016 HG19 1.15E+09 427948 43% 25% 35% 110.0 0.82% 51%0.444 0.072 BRCA Prototype 9C_BRCA 8.24 Apr. 15, 2016 HG19 1.18E+09424163 43% 26% 35% 113.0 0.87% 52% 0.454 0.082 BRCAA comparision of the raw error rates demonstrated equivalency betweenthe two imaging reagents. See, FIG. 8. The SC-P9C imaging reagentsequencing metrics were also compared between the HEPES buffer and theTRIS buffer using a 157 cycles non-APF/88 tile protocol on a DHMG02 BRCAgene panel. See, Table 4.

TABLE 4 Sequence Metrics Comparison Of SC-P9C To Baseline IB On A BRCAGene Panel Comparing HEPES Buffer To TRIS Buffer Output Run Condition GRSample ID Run date Type Cycles (MFST) Beads/tile Ref_Baseline 8.24FC1_DHMG02 Apr. 26, 2016 HG19 BRCA 150 1.28E+09 419417 Ref_Baseline 8.24FC2_DHMG02 Apr. 26, 2016 HG19 BRCA 150 1.34E+09 409874 IB_P9CV2_HEPES8.26 FC1_DHMG02 Apr. 26, 2016 HG19 BRCA 150 1.37E+09 417428IB_P9CV2_HEPES 8.26 FC2_DHMG02 Apr. 26, 2016 HG19 BRCA 150 1.35E+09423869 Proto9C_V2_Tris 8.26 FC1_DHMG02 Apr. 15, 2016 HG19 BRCA 1501.07E+09 428096 Proto9C_V2_Tris 8.26 FC2_DHMG02 Apr. 15, 2016 HG19 BRCA150 1.10E+09 422093 Proto9C_V2_Tris 8.24 FC1_DHMG02 Apr. 15, 2016 HG19BRCA 150 1.03E+09 427948 Proto9C_V2_Tris 8.24 FC2_DHMG02 Apr. 15, 2016HG19 BRCA 150 1.08E+09 424163 % % % Error % Run Condition Live MappedPolyclonal AVG RL (MFST) Perfect Lead Lag Ref_Baseline 51% 31% 36% 110.80.83% 56% 0.490 0.024 Ref_Baseline 53% 33% 36% 113.2 0.83% 56% 0.4900.035 IB_P9CV2_HEPES 49% 31% 35% 112.6 0.79% 57% 0.420 0.040IB_P9CV2_HEPES 50% 32% 35% 114.5 0.76% 58% 0.449 0.046 Proto9C_V2_Tris44% 26% 36% 109.0 0.96% 51% 0.477 0.061 Proto9C_V2_Tris 45% 26% 36%111.5 0.94% 52% 0.446 0.084 Proto9C_V2_Tris 43% 25% 35% 108.7 1.03% 50%0.444 0.072 Proto9C_V2_Tris 43% 26% 35% 112.3 1.02% 50% 0.454 0.082The data demonstrate that the SC-P 9C imaging reagent formulated in aHEPES buffer outperforms the SC-P 9C imaging reagent formulated in TrisHCl. Similarly, the raw error rate is less using a HEPES buffer ascompared to a Tris HCl and is more similar to the baseline IB. See, FIG.9A and 9B.

These data demonstrate that photoprotective imaging reagents withprotocatechuic ethyl ester is superior to photoprotective imagingreagents with gentisic acid in regards to signal stability and quality.Although it is not necessary to understand the mechanism of aninvention, it is believed that signal stability and quality plays a rolein sequencing performance quality. Nonetheless, both gentisic- andprotocatechuic-based cocktail chemistries (i.e., SC-P 7B and SC-P 9C,respectively) are expected to benchmark competitively in regards tocomparative performance for long read sequencing. From a manufacturingperspective, however, photoprotective imaging reagents withprotocatechuic ethyl ester may be preferable than photoprotectiveimaging reagents with gentisic acid due to better flexibility and costeffectiveness of making the formulation.

Further studies were performed to determine if decreasing carnitineconcentration in a photoprotective imaging reagent (e.g., betweenapproximately 50 mM to 5 mM) influences sequencing performance. Thecomposition of the tested photoprotective carnitine imaging reagents(e.g., SC-P9, SC-P9B and SC-P9C) are as follows:

Prototype 9

50 mM Tris buffer pH 8.5 50 mM L-Carnitine 15 mM Trolox 20 mMProtocatechuic Acid Ethyl Ester

Prototype 9B

50 mM Tris buffer pH 8.5 15 mM L-Carnitine 15 mM Trolox 20 mMProtocatechuic Acid Ethyl Ester

Prototype 9D

50 mM Tris buffer pH 7.8  5 mM L-Carnitine 15 mM Trolox 20 mMProtocatechuic Acid Ethyl EsterThe sequencing runs (8.17, 8.24, 8.26) setups comprised 132 cycles forboth the reference and/or baseline D3 reagent and the photoprotective D3reagent using samples NA12878/101X (ID: TP03) or NA12878/BRCA (ID:DHMG02). The data show that 15 mM Carnitine is provides an optimalworking concentration based on average read length and signal retention.See, Table 5.

TABLE 5 ADAM Results From Carnitine Concentration Analysis Output RunCondition GR Sample ID Run date Type Cycles (MFST) Beads/tile % LiveIB_baseline 8.26 FC1 8.26 TP03_FC1 Mar. 30, 2016 HG19 101X 125 1.18E+09446379.5 48.8% IB_baseline 8.26 FC2 8.26 TP03_FC2 Mar. 30, 2016 HG19101X 125 1.20E+09 414836.1 51.2% IB_baseline 8.17 FC1 8.17 FC1_TP03 Apr.4, 2016 HG19 101X 125 1.27E+09 426583.5 53.6% IB_baseline 8.17 FC2 8.17FC2_TP03 Apr. 4, 2016 HG19 101X 125 1.26E+09 426191.8 52.7% IB_SC-P9_FC18.26 FC1_TP03 Apr. 4, 2016 HG19 101X 125 1.21E+09 424152.8 52.4%IB_SC-P9_FC2 8.26 FC2_TP03 Apr. 4, 2016 HG19 101X 125 1.22E+09 432521.252.8% IB_SC-P9B_FC1 8.26 FC1_TP03 Apr. 11, 2016 HG19 101X 125 1.16E+09419886.9 49.6% IB_SC-P9B_FC2 8.26 FC2_TP03 Apr. 11, 2016 HG19 101X 1251.16E+09 414822.6 49.9% Baseline_BRCA_AGR 8.17 1_DHMGO Apr. 15, 2016HG19 BRCA 125 1.01E+09 426294.1 47.1% Baseline_BRCA_AGR 8.17 2_DHMGOApr. 15, 2016 HG19 BRCA 125 1.03E+09 424932.8 45.1% IB_Proto9D_BRCA_AGR8.26 1_DHMGO Apr. 19, 2016 HG19 BRCA 125 9.85E+08 428784.6 44.9%IB_Proto9D_BRCA_AGR 8.26 2_DHMGO Apr. 19, 2016 HG19 BRCA 125 1.02E+09430237.1 45.6% Run Condition % BC % Mapped AVG RL Error Rate % PerfectLead Lag Notes IB_baseline 8.26 FC1 73.0% 30.5% 99.0 0.55% 69.1% 0.4150.139 baseline 101X IB_baseline 8.26 FC2 73.6% 32.5% 100.9 0.54% 69.3%0.378 0.149 baseline 101X IB_baseline 8.17 FC1 74.3% 34.1% 99.4 0.58%67.6% 0.470 0.109 baseline 101X IB_baseline 8.17 FC2 73.6% 33.2% 100.80.59% 66.6% 0.423 0.127 baseline 101X IB_SC-P9_FC1 74.8% 33.0% 97.90.53% 69.7% 0.409 0.111 50 mM camitine IB_SC-P9_FC2 75.0% 33.1% 97.00.56% 68.3% 0.405 0.122 50 mM camitine IB_SC-P9B_FC1 73.3% 31.7% 98.60.55% 69.0% 0.389 0.126 15 mM camitine IB_SC-P9B_FC2 73.5% 31.9% 99.20.54% 69.2% 0.389 0.123 15 mM camitine Baseline_BRCA_AGR   71%   26%103.5 0.68% 64.4% 0.473 0.109 baseline_BRCA Baseline_BRCA_AGR   72%  27% 104.1 0.70% 63.2% 0.431 0.117 baseline_BRCA IB_Proto9D_BRCA_AGR  71%   27% 97.2 0.69% 63.6% 0.425 0.101 5 mM camitineIB_Proto9D_BRCA_AGR   71%   27% 99.0 0.68% 63.5% 0.425 0.111 5 mMcamitine

In particular, reduced carnitine concentration lowers data output (MFST)in a concentration-dependent manner in both the 101x gene panel and theBRCA gene panel. See, FIG. 10. This output data was collected underconditions where the percent perfect parameters went unchanged ascompared to the reference IB reagent. See, FIG. 11. The average readlength, however, was seen to be lower overall when the photoprotectiveimaging reagents contain carnitine. See, FIG. 12. Nonetheless, there wasno effect of photoprotective imaging reagents containing carnitine onpercent error rate when compared to the reference D3 reagent. See, FIG.13. There were differences, however, between photoprotective imagingreagents having different carnitine concentrations regarding the rawerror rate parameter. For example, the SC-9 IB reagent (50 mM carnitine)and SC-9B D3 reagent (15 mM carnitine) had raw error rates similar tothe reference D3 reagent. See, FIG. 14A. The SC-9D D3 reagent (5 mMcarnitine), however, showed a higher raw error rate as compared to thereference IB reagent. See, FIG. 14B. This data pattern is seen for thedistribution of read lengths between the tested imaging reagents. TheSC-9 IB reagent (50 mM carnitine) and SC-9B D3 reagent (15 mM carnitine)had read length distributions that were similar to the reference D3reagent. See, FIG. 15A. The SC-9D D3 reagent (5 mM carnitine), however,showed a read length distribution that was biased to the early cycles,and somewhat lower, as compared to the reference IB reagent. See, FIG.15B. Signal retention for all nucleotides was reduced in the presence ofcarnitine, as shown by the best signal retention with the lowercarnitine concentration photoprotective IB reagent (e.g., SC-9B, 15 mM).See, FIG. 16.

Overall, the data presented herein shows that photoprotective SC-P 7B IBreagent and SC-P 9C IB reagent perform similarly to a conventionalimaging buffer reagent (e.g., baseline IB) and deliver an average readlength minimum requirement that is compatible with state of the art genereaders. Specifically, the data show that photoprotective imaging bufferreagents as contemplated herein are efficient when scanning an averageread length of approximately 110 bp as compared to the optimal scanningrange of state of the art gene readers of between approximately 110-130bp.

Experimental EXAMPLE I Photoprotective Imaging Formulation Stability andPreservation

Components in various photoprotective imaging mixtures as describedherein have been tested for solubility and stability againstprecipitation and discoloration in imaging solution formulation usingTris HCl as the base buffer. The optimal concentration windows for thevarious components have been found to be the following: Carnitine (5-50mM); Trolox (5-15 mM); 2,5-Dihydroxybenzoic Acid (10-50 mM); and3,4-Dihydroxybenzoic Acid Ethyl Ester (Protocatechuate EthylEster)(10-20 mM).

EXAMPLE II Composition and Formulation of Photoprotective ImagingReagent SC-P 7B

The following example describes the preparation of approximately twohundred (200) milliliters of imaging reagent that would be expected tosupport a 4FC/157 cycle SBS method.

-   -   50 mM Tris buffer: 121.4 g/mol =1.21g (Sigma: Cat #T1378-1kg)    -   50 mM L Carnitine: 197.66 g/mol =1.98g (Sigma: Cat #CO283-100G)    -   15 mM Trolox: 250.29 g/mol =0.75g (Sigma: Cat #238813-5G)    -   50 mM Gentisic Acid 176.1 g/mol =1.76 g (Sigma: G5129-10G)    -   1. Dissolve Tris Base in 180 mL milliQ water.    -   2. Add Trolox to the Tris buffer from Step 1.    -   3. Add L Carnitine to the above solution.    -   4. Add Gentisic acid sodium salt hydrate and dissolve.    -   5. Checked pH: ˜4    -   6. Adjusted pH to 7.8 with 10M NaOH solution.    -   7. Bring total volume to 200 mL with milliQ water.    -   8. Filter sterilize.    -   9. Split imaging buffer into 2 conical tubes (approx. 25 mL        aliquots each) for single FC GR run.

EXAMPLE III Composition and Formulation of Photoprotective ImagingReagent 9CV2T

The following example describes the preparation of approximately twohundred (200) milliliters of imaging reagent.

-   -   50 mM Tris buffer: 121.4 g/mol =0.607g (Sigma: Cat #T1378-1kg)    -   15 mM L Carnitine: 197.66 g/mol =0.296g (Sigma: Cat #CO238-100G)    -   15 mM Trolox: 250.29 g/mol =0.375g (Sigma: Cat #238813-5G)    -   10 mM Protocatechuic Acid Ethyl Ester 182.17 g/mol =182.17 mg        milligrams (Sigma: Cat #E24859-5G)    -   1. Dissolve Tris Base in 75 mL milliQ water.    -   2. Add Trolox and dissolve completely    -   3. Added Protocatechuic Acid    -   4. Add L Carnitine and dissolve completely.    -   5. Checked pH:    -   6. Adjusted pH to 8.5 with 10M NaOH.    -   7. Optional: Sonicate until well mixed.    -   8. Bring total volume to 100 mL with milliQ water.    -   9. Filter sterilize.

EXAMPLE IV Composition and Formulation of Photoprotective ImagingReagent 9CV2H

The following example describes the preparation of approximately onehundred (100) milliliters of imaging reagent.

-   -   100 mM HEPES: 238.3 gr/mole=2.39g (Sigma: Cat #H4034)    -   15 mM L Carnitine: 197.66 g/mol=0.296g (Sigma: Cat #CO283-100G)    -   15 mM Trolox: 250.29 g/mol=0.375g (Sigma: Cat #238813-5G)    -   10 mM Protocatechuic Acid Ethyl Ester 182.17 g/mol=0.182g        (Sigma: Cat #E24859-5G)

1Liter 100 mM HEPES 23.9 gr HEPES

Dissolve in MilliQ water- final volume 1 LiterpH was adjusted to 7.0.

-   -   1. Obtain 75 mL HEPES buffer (see below).    -   2. Add Trolox and dissolve completely    -   3. Added Protocatechuic Acid.    -   4. Add L Carnitine and dissolve completely.    -   5. Checked pH: ˜5    -   6. Adjusted pH to 7.5 with 10M NaOH.    -   7. Optional: Sonicate until well mixed.    -   8. Bring total volume to 100 mL with milliQ water.    -   9. Filter sterilize.

We claim:
 1. A method of incorporating labeled nucleotides, comprising:a) providing; i) a plurality of nucleic acid primers and templatemolecules, ii) a polymerase, iii) an imaging reagent comprising aphotoprotective mixture of compounds, and iv) a plurality of nucleotideanalogues wherein at least a portion of said nucleotide analogues islabeled with a label attached through a cleavable linker to the base; b)hybridizing at least a portion of said primers to at least a portion ofsaid template molecules so as to create hybridized primers; c)incorporating a first labeled nucleotide analogue with said polymeraseinto at least a portion of said hybridized primers so as to createextended primers comprising an incorporated labeled nucleotide analogue;and d) imaging said incorporated labeled nucleotide analogue in thepresence of said imaging reagent.
 2. The method of claim 1, wherein saidphotoprotective mixture comprises at least one fluorescence quenchinginhibitor.
 3. The method of claim 2, wherein said at least onefluorescence quenching inhibitor is trolox.
 4. The method of claim 1,wherein said photoprotective mixture further comprises at least oneantioxidant and at least one radical scavenger compound.
 5. The methodof claim 4, wherein said at least one antioxidant is selected from thegroup consisting of gentisic acid, protocatechuic acid andprotocatechuate ethyl ester.
 6. The method of claim 4, wherein said atleast one radical scavenger compound is carnitine.
 7. The method ofclaim 1, further comprising step (e) incorporating a second nucleotideanalogue with said polymerase into at least a portion of said extendedprimers.
 8. The method of claim 1, wherein said label is fluorescent. 9.An imaging reagent comprising at least one antioxidant, at least onefluorescence quenching inhibitor and a buffer.
 10. The imaging reagentof claim 9, wherein said at least one antioxidant comprises compoundsselected from the group consisting of gentisic acid, protocatechuic acidand protocatechuate ethyl ester.
 11. The imaging reagent of claim 9,further comprising at least one radical scavenger.
 12. The imagingreagent of claim 11, wherein said at least one radical scavenger iscarnitine.
 13. The imaging reagent of claim 9, wherein said fluorescencequenching inhibitor is trolox.
 14. The imaging reagent of claim 9,wherein said buffer is a TRIS buffer.
 15. The imaging reagent of claim9, wherein said buffer is a HEPES buffer.
 16. A kit, comprising: i) afirst container comprising an imaging reagent comprising at least oneantioxidant, at least one fluoresence quenching inhibitor and a bufferand ii) a second container comprising a plurality of nucleotideanalogues wherein at least a portion of said nucleotide analogues islabeled with a label attached through a cleavable linker to the base.17. The kit of claim 16, wherein said first container further comprisesat least one radical scavenger.
 18. The kit of claim 17, wherein said atleast one radical scavenger is carnitine.
 19. The kit of claim 16,wherein said at least one fluorescence quenching inhibitor is trolox.20. The kit of claim 16, wherein said buffer is a TRIS buffer.
 21. Thekit of claim 16, wherein said buffer is a HEPES buffer.
 22. A systemcomprising a solution of primers hybridized to a template comprising aplurality of nucleotide analogues attached to a cleavable label and animaging reagent comprising at least one antioxidant, at least onefluorescent quenching inhibitor and a buffer.
 23. The system of claim22, wherein said hybridized primers and said template are immobilized.24. The system of claim 22, wherein said hybridized primers and saidtemplate are in a flow cell.
 25. The system of claim 22, wherein saidimaging agent further comprises at least one radical scavenger.
 26. Thesystem of claim 25, wherein said at least one radical scavenger iscarnitine.
 27. The system of claim 22, wherein said at least onefluorescence quenching inhibitor is trolox.
 28. The system of claim 22,wherein said buffer is a TRIS buffer.
 29. The system of claim 22,wherein said buffer is a HEPES buffer.
 30. An imaging reagentcomprising: i) a TRIS HCl buffer; ii) carnitine ranging in concentrationbetween approximately 5-50 mM; iii) trolox ranging in concentrationbetween approximately 5-15 mM; iv) 2,5 dihydroxybenzoic acid ranging inconcentration between approximately 10 -50 mM; and v) 3,4,dihydroxybenzoic acid ethyl ester ranging in concentration betweenapproximately 10-20 mM.